Timbuktu, Mali — The first thing Islamist militants did upon commandeering Timbuktu’s Ahmed Baba Institute for Higher Learning and Islamic Research last April was change the locks. Their parting act last week was to burn some of the institute’s medieval manuscripts.

"All this time, we were the only state service they didn’t destroy,” says Abdoulaye Cissé, an archaeology professor and acting director of the institute. Mr. Cissé sits on a bench in the institute’s enclosure, a temple-like complex with inner courts and alleys partly open to the sky, as the wind tosses ashes from a pile near his feet.

During their nine months in control of Timbuktu, Islamists wrecked some of the city’s historic sites and terrorized its people. Last week, as French and Malian troops advanced, they torched around 2,000 of the Baba Ahmed Institute’s manuscripts – a parting shot that locals are still trying to understand.

Many of the Islamist militants in Mali share a violent form of salafism, an ultraconservative reformist trend in Islam that seeks to emulate the religion’s earliest generations. That means following core texts to the letter, while largely rejecting 14 centuries of Islamic thought, scholarship and spirituality.

In Timbuktu, that translated largely to oppression and vandalism under rule by Ansar al-Din and Al Qaeda in the Islamic Maghreb (AQIM), two of three Islamist militant groups that overran Mali’s north last year.

Beatings, mutilation

Smoking and music were punished with beatings, and theft with cutting off the accused person’s hand. Last summer, militants demolished the graves of Sufi holy men venerated here as links to God – a common practice in Islamic mysticism that looks to some conservatives like polytheism.

Yet few, if any, in Timbuktu expected the city’s manuscripts to be targeted. For months, militants – including those who took up residence in the Baba Ahmed Institute – made no move against them.

Timbuktu’s wealth of Islamic manuscripts - estimated in the scores of thousands - date to its role as a trading hub and center of learning in the late Middle Ages. The city reached a zenith in the 16th century, when books were among the most precious commodities and scholars were supported by the state.

The best-known scholar was perhaps Ahmed Baba, who produced dozens of works mainly on theology and Islamic jurisprudence. But meanwhile, up north, trouble was brewing. Invasion by an army of the Moroccan sultan in 1591 saw scholars including Baba Ahmed arrested or deported and Timbuktu slid into decline.

In recent decades, the Malian government and family-owned libraries have worked to restore Timbuktu’s manuscripts and present them to the world. The state-run Baba Ahmed Institute, as well as some private libraries, have facilities to restore, catalog, and scan manuscripts.

“Every manuscript is important, even if it’s just a scrap of paper – even if it’s only two or three words,” says Hamou Mohamed Dédeou, a manuscript specialist in Timbuktu who has worked with the Baba Ahmed Institute and advised foreign scholars.

Rich texts

It was in this spirit that Mr. Dédeou wrote “The Role of Symbols and Tables in Applying the Studies of the Ancients,” an explanatory work aimed at helping students appreciate the richness of some texts.

In one example, a seemingly nonsensical couplet by Ahmed Baba is revealed as a mnemonic device. Letters represent numbers, which in turn count the steps to take along one’s own shadow in various months to calculate certain prayer times.

The couplet ends with the phrase “And with the rest, don’t be stubborn.” Dédeou likes to understand it thus: “Don’t be stubborn concerning what you don’t know.”

While no threat arose against Timbuktu’s manuscripts in the early days of the Islamist occupation, curators weren’t taking chances. There was a general sense of lawlessness. Cissé had most of the Baba Ahmed Institute’s roughly 30,000 texts spirited out of town and sent up the Niger River in pirogues; Abdelkader Haidara, a private curator, arranged for manuscripts to be hidden in houses.

Then came turmoil this month, as an Islamist push south provoked a counter-offensive by French and Malian forces. In town after town, militants cleared out as their enemies advanced.

Last Thursday morning, people living near the Baba Ahmed Institute awoke to see smoke rising from within. In an adjacent neighborhood, Lithnin Dicko, one of the institute’s two watchmen – then jobless thanks to the Islamist occupancy – was about to eat breakfast when a man appeared at his house.

“Come quick! The manuscripts are burning!” the man said. Mr. Dicko dashed over to the Institute, through the door, down an alleyway and around a corner, to find a small courtyard full of flame. “There was nothing I could do but watch the manuscripts burn,” he says.

This morning, a tumble of plastic manuscript cases with serial numbers on the spines lay in the courtyard beside a pile of ashes. Staff were busy changing the locks. An alarm that Dicko says was somehow triggered by Islamists couldn't be switched off, and was still wailing.

The loss isn’t total, says Cissé. Manuscripts have been destroyed and the computers holding their scanned images stolen, but there are back-up scans at the institute’s facility in Bamako, the capital. Yet something of Timbuktu’s soul has been wounded.

“Human beings want to be in contact with what is original,” says Dédeou. “One wants to touch. That is what we will miss.”